mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-23 13:58:12 +08:00
wire up geneset reducer (#2082)
* first cut at GET /genesets route * update existing tests to match code changes * more GET /genesets and initial tests * add missing test fixture * geneset validation accepts OTA format * genesets route: better error handling, more tests * lint * genesets reducer and initial load * fix lint * add autosave support for genesets * remove debug logging * fix typo * fix another typo * update smoke test config for genesets * smoke test fixes * more fiddling with smoke tests
This commit is contained in:
Bruce Martin
@@ -0,0 +1,524 @@
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import genesetsReducer from "../../src/reducers/genesets";
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describe("initial reducer state", () => {
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test("some other action", () => {
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expect(genesetsReducer(undefined, { type: "foo" })).toMatchObject({
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initialized: false,
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lastTid: undefined,
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genesets: new Map(),
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});
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});
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});
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describe("geneset: initial load", () => {
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test("missing JSON response", () => {
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expect(() =>
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genesetsReducer(undefined, {
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type: "geneset: initial load",
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})
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).toThrow("missing or malformed JSON response");
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});
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test("empty geneset", () => {
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expect(
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genesetsReducer(undefined, {
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type: "geneset: initial load",
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data: {
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tid: 0,
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genesets: [],
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},
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})
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).toMatchObject({
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initialized: true,
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lastTid: 0,
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genesets: new Map(),
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});
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});
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test("non-empty geneset", () => {
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expect(
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genesetsReducer(undefined, {
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type: "geneset: initial load",
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data: {
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tid: 99,
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genesets: [
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{
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geneset_name: "G1",
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genes: [{ gene_symbol: "F5" }],
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},
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{
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geneset_name: "G2",
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geneset_description: "G2 desc",
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genes: [{ gene_symbol: "F6" }],
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},
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{
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geneset_name: "G3",
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geneset_description: "G3 desc",
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genes: [{ gene_symbol: "F7", gene_description: "gene desc" }],
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},
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],
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},
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})
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).toMatchObject({
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initialized: true,
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lastTid: 99,
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genesets: new Map([
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[
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"G1",
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{
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genesetName: "G1",
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genesetDescription: "",
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genes: new Map([["F5", { geneSymbol: "F5", geneDescription: "" }]]),
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},
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],
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[
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"G2",
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{
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genesetName: "G2",
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genesetDescription: "G2 desc",
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genes: new Map([["F6", { geneSymbol: "F6", geneDescription: "" }]]),
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},
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],
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[
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"G3",
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{
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genesetName: "G3",
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genesetDescription: "G3 desc",
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genes: new Map([
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["F7", { geneSymbol: "F7", geneDescription: "gene desc" }],
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]),
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},
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],
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]),
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});
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});
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});
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describe("geneset: create", () => {
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const initialState = genesetsReducer(undefined, {
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type: "geneset: initial load",
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data: {
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tid: 0,
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genesets: [],
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},
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});
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test("simple create", () => {
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expect(
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genesetsReducer(initialState, {
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type: "geneset: create",
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genesetName: "a geneset",
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genesetDescription: "",
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})
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).toMatchObject({
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...initialState,
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genesets: new Map([
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[
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"a geneset",
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{
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genesetName: "a geneset",
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genesetDescription: "",
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genes: new Map(),
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},
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],
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]),
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});
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});
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test("error - duplicate name", () => {
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expect(() => {
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genesetsReducer(
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genesetsReducer(initialState, {
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type: "geneset: create",
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genesetName: "foo",
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genesetDescription: "foo",
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}),
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{
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type: "geneset: create",
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genesetName: "foo",
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genesetDescription: "bar",
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}
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);
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}).toThrow("name already defined");
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});
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test("error - missing required action values", () => {
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expect(() => {
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genesetsReducer(initialState, {
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type: "geneset: create",
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genesetDescription: "foo",
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});
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}).toThrow();
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expect(() => {
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genesetsReducer(initialState, {
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type: "geneset: create",
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genesetName: "foo",
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});
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}).toThrow("name or description unspecified");
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});
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});
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describe("geneset: delete", () => {
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const initialState = genesetsReducer(undefined, {
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type: "geneset: initial load",
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data: {
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tid: 0,
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genesets: [],
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},
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});
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test("simple delete", () => {
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expect(
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genesetsReducer(
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genesetsReducer(initialState, {
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type: "geneset: create",
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genesetName: "foo",
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genesetDescription: "foo",
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}),
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{
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type: "geneset: delete",
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genesetName: "foo",
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}
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)
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).toMatchObject({
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initialized: true,
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lastTid: 0,
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genesets: new Map(),
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});
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});
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test("error - missing name", () => {
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expect(() => {
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genesetsReducer(initialState, {
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type: "geneset: delete",
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genesetName: "foo",
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});
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}).toThrow("name does not exist");
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});
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});
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describe("geneset: update", () => {
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const initialState = genesetsReducer(undefined, {
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type: "geneset: initial load",
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data: {
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tid: 0,
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genesets: [],
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},
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});
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test("simple update", () => {
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expect(
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genesetsReducer(
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genesetsReducer(
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genesetsReducer(initialState, {
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type: "geneset: create",
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genesetName: "foo1",
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genesetDescription: "foo1",
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}),
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{
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type: "geneset: create",
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genesetName: "foo2",
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genesetDescription: "foo2",
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}
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),
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{
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type: "geneset: update",
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genesetName: "foo1",
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update: {
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genesetName: "bar",
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genesetDescription: "bar",
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},
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}
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)
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).toMatchObject({
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initialized: true,
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lastTid: 0,
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genesets: new Map([
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[
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"bar",
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{ genesetName: "bar", genesetDescription: "bar", genes: new Map() },
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],
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[
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"foo2",
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{ genesetName: "foo2", genesetDescription: "foo2", genes: new Map() },
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],
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]),
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});
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});
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test("error - unknown name", () => {
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expect(() => {
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genesetsReducer(initialState, {
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type: "geneset: update",
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genesetName: "foo",
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update: {
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genesetName: "foo",
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genesetDescription: "bar",
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},
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});
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}).toThrow("name unspecified or does not exist");
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});
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test("error - duplicate name", () => {
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expect(() => {
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genesetsReducer(
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genesetsReducer(initialState, {
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type: "geneset: create",
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genesetName: "foo",
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genesetDescription: "foo",
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}),
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{
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type: "geneset: update",
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genesetName: "foo",
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update: {
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genesetName: "foo",
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genesetDescription: "foo",
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},
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}
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);
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}).toThrow("update specified existing name");
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});
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});
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describe("geneset: add genes", () => {
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const initialState = genesetsReducer(
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genesetsReducer(undefined, {
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type: "geneset: initial load",
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data: {
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tid: 0,
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genesets: [],
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},
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}),
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{
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type: "geneset: create",
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genesetName: "test",
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genesetDescription: "",
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}
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);
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test("add a gene", () => {
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expect(
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genesetsReducer(initialState, {
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type: "geneset: add genes",
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genesetName: "test",
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genes: [{ geneSymbol: "F5" }],
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})
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).toMatchObject({
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...initialState,
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genesets: new Map([
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[
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"test",
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{
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genesetName: "test",
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genesetDescription: "",
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genes: new Map([["F5", { geneSymbol: "F5", geneDescription: "" }]]),
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},
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],
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]),
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});
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expect(
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genesetsReducer(initialState, {
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type: "geneset: add genes",
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genesetName: "test",
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genes: [
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{ geneSymbol: "F5", geneDescription: "desc" },
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{ geneSymbol: "SET1", geneDescription: "" },
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],
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})
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).toMatchObject({
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...initialState,
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genesets: new Map([
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[
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"test",
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{
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genesetName: "test",
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genesetDescription: "",
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genes: new Map([
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["F5", { geneSymbol: "F5", geneDescription: "desc" }],
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["SET1", { geneSymbol: "SET1", geneDescription: "" }],
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]),
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},
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],
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]),
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});
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});
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test("no such geneset error", () => {
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expect(() => {
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genesetsReducer(initialState, {
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type: "geneset: add genes",
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genesetName: "mumble",
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genes: [],
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});
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}).toThrow("geneset name does not exist");
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});
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});
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describe("geneset: delete genes", () => {
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const initialState = genesetsReducer(
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genesetsReducer(
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genesetsReducer(undefined, {
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type: "geneset: initial load",
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data: {
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tid: 0,
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genesets: [],
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},
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}),
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{
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type: "geneset: create",
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genesetName: "test",
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genesetDescription: "",
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}
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),
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{
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type: "geneset: add genes",
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genesetName: "test",
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genes: [{ geneSymbol: "F5" }],
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}
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);
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test("simple", () => {
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expect(
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genesetsReducer(initialState, {
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type: "geneset: delete genes",
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genesetName: "test",
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geneSymbols: ["F5"],
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})
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).toMatchObject({
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...initialState,
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genesets: new Map([
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[
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"test",
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{
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genesetName: "test",
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genesetDescription: "",
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genes: new Map(),
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},
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],
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]),
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});
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});
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test("no such geneset error", () => {
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expect(() => {
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genesetsReducer(initialState, {
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type: "geneset: delete genes",
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genesetName: "mumble",
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geneSymbols: [],
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});
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}).toThrow("name does not exist");
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});
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});
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describe("geneset: set gene description", () => {
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const initialState = genesetsReducer(
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genesetsReducer(
|
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genesetsReducer(undefined, {
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type: "geneset: initial load",
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data: {
|
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tid: 0,
|
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genesets: [],
|
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},
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}),
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{
|
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type: "geneset: create",
|
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genesetName: "test",
|
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genesetDescription: "",
|
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}
|
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),
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{
|
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type: "geneset: add genes",
|
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genesetName: "test",
|
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genes: [{ geneSymbol: "F5" }],
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}
|
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);
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|
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test("simple set", () => {
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expect(
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genesetsReducer(initialState, {
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type: "geneset: set gene description",
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genesetName: "test",
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update: {
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geneSymbol: "F5",
|
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geneDescription: "mumble",
|
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},
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})
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).toMatchObject({
|
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...initialState,
|
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genesets: new Map([
|
||||
[
|
||||
"test",
|
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{
|
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genesetName: "test",
|
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genesetDescription: "",
|
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genes: new Map([
|
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["F5", { geneSymbol: "F5", geneDescription: "mumble" }],
|
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]),
|
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},
|
||||
],
|
||||
]),
|
||||
});
|
||||
});
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|
||||
test("no such geneset error", () => {
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expect(() => {
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genesetsReducer(initialState, {
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type: "geneset: set gene description",
|
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genesetName: "does not exist",
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update: {
|
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geneSymbol: "F5",
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geneDescription: "mumble",
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},
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||||
});
|
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}).toThrow("geneset name does not exist");
|
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});
|
||||
|
||||
test("no such gene error", () => {
|
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expect(() => {
|
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genesetsReducer(initialState, {
|
||||
type: "geneset: set gene description",
|
||||
genesetName: "test",
|
||||
update: {
|
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geneSymbol: "NO SUCH GENE",
|
||||
geneDescription: "mumble",
|
||||
},
|
||||
});
|
||||
}).toThrow("no such gene");
|
||||
});
|
||||
});
|
||||
|
||||
describe("geneset: set tid", () => {
|
||||
test("simple set", () => {
|
||||
expect(
|
||||
genesetsReducer(undefined, {
|
||||
type: "geneset: set tid",
|
||||
tid: 1,
|
||||
})
|
||||
).toMatchObject({ lastTid: 1 });
|
||||
});
|
||||
|
||||
test("not a number error", () => {
|
||||
expect(() => {
|
||||
genesetsReducer(
|
||||
{ lastTid: 1 },
|
||||
{
|
||||
type: "geneset: set tid",
|
||||
tid: "0",
|
||||
}
|
||||
);
|
||||
}).toThrow("must be a positive integer");
|
||||
});
|
||||
|
||||
test("decrement error", () => {
|
||||
expect(() => {
|
||||
genesetsReducer(
|
||||
{ lastTid: 1 },
|
||||
{
|
||||
type: "geneset: set tid",
|
||||
tid: 0,
|
||||
}
|
||||
);
|
||||
}).toThrow("may not be decremented");
|
||||
});
|
||||
});
|
||||
@@ -387,3 +387,96 @@ export const saveObsAnnotationsAction = () => async (dispatch, getState) => {
|
||||
});
|
||||
}
|
||||
};
|
||||
|
||||
export const saveGenesetsAction = () => async (dispatch, getState) => {
|
||||
const state = getState();
|
||||
|
||||
// bail if gene sets not available, or in readonly mode.
|
||||
const { config } = state;
|
||||
const genesetsAreAvailable =
|
||||
config?.parameters?.["annotations_genesets"] ?? false;
|
||||
const genesetsReadonly =
|
||||
config?.parameters?.["annotations_genesets_readonly"] ?? true;
|
||||
if (!genesetsAreAvailable || genesetsReadonly) {
|
||||
// our non-save was completed!
|
||||
return dispatch({
|
||||
type: "autosave: genesets complete",
|
||||
lastSavedGenesets: state.genesets,
|
||||
});
|
||||
}
|
||||
|
||||
const { lastTid, genesets: lastGenesets } = state.genesets;
|
||||
|
||||
/* Create the JSON OTA data structure */
|
||||
const tid = (lastTid ?? 0) + 1;
|
||||
const genesets = [];
|
||||
for (const [name, gs] of lastGenesets) {
|
||||
// const genes = Array.from(gs.genes.values());
|
||||
const genes = [];
|
||||
for (const g of gs.genes.values()) {
|
||||
genes.push({
|
||||
gene_symbol: g.geneSymbol,
|
||||
gene_description: g.geneDescription,
|
||||
});
|
||||
}
|
||||
genesets.push({
|
||||
geneset_name: name,
|
||||
geneset_description: gs.genesetDescription,
|
||||
genes,
|
||||
});
|
||||
}
|
||||
const ota = {
|
||||
tid,
|
||||
genesets,
|
||||
};
|
||||
|
||||
/* Save to server */
|
||||
try {
|
||||
const {
|
||||
dataCollectionNameIsReadOnly,
|
||||
dataCollectionName,
|
||||
} = state.annotations;
|
||||
const queryString =
|
||||
!dataCollectionNameIsReadOnly && !!dataCollectionName
|
||||
? `?annotation-collection-name=${encodeURIComponent(
|
||||
dataCollectionName
|
||||
)}`
|
||||
: "";
|
||||
|
||||
const res = await fetch(
|
||||
`${globals.API.prefix}${globals.API.version}genesets${queryString}`,
|
||||
{
|
||||
method: "PUT",
|
||||
headers: new Headers({
|
||||
Accept: "application/json",
|
||||
"Content-Type": "application/json",
|
||||
}),
|
||||
body: JSON.stringify(ota),
|
||||
credentials: "include",
|
||||
}
|
||||
);
|
||||
if (!res.ok) {
|
||||
return dispatch({
|
||||
type: "autosave: genesets error",
|
||||
message: `HTTP error ${res.status} - ${res.statusText}`,
|
||||
res,
|
||||
});
|
||||
}
|
||||
return Promise.all([
|
||||
dispatch({
|
||||
type: "autosave: genesets complete",
|
||||
lastSavedGenesets: genesets,
|
||||
}),
|
||||
dispatch({
|
||||
type: "geneset: set tid",
|
||||
tid,
|
||||
}),
|
||||
]);
|
||||
} catch (error) {
|
||||
return dispatch({
|
||||
type: "autosave: genesets error",
|
||||
message: error.toString(),
|
||||
error,
|
||||
});
|
||||
}
|
||||
};
|
||||
|
||||
@@ -52,6 +52,27 @@ async function userInfoFetch(dispatch) {
|
||||
});
|
||||
}
|
||||
|
||||
async function genesetsFetch(dispatch, config) {
|
||||
/* request genesets ONLY if the backend supports the feature */
|
||||
const defaultResponse = {
|
||||
genesets: [],
|
||||
tid: 0,
|
||||
};
|
||||
if (config?.parameters?.["annotations_genesets"] ?? false) {
|
||||
fetchJson("genesets").then((response) => {
|
||||
dispatch({
|
||||
type: "geneset: initial load",
|
||||
data: response ?? defaultResponse,
|
||||
});
|
||||
});
|
||||
} else {
|
||||
dispatch({
|
||||
type: "geneset: initial load",
|
||||
data: defaultResponse,
|
||||
});
|
||||
}
|
||||
}
|
||||
|
||||
function prefetchEmbeddings(annoMatrix) {
|
||||
/*
|
||||
prefetch requests for all embeddings
|
||||
@@ -76,6 +97,8 @@ const doInitialDataLoad = () =>
|
||||
userInfoFetch(dispatch),
|
||||
]);
|
||||
|
||||
genesetsFetch(dispatch, config);
|
||||
|
||||
const baseDataUrl = `${globals.API.prefix}${globals.API.version}`;
|
||||
const annoMatrix = new AnnoMatrixLoader(baseDataUrl, schema.schema);
|
||||
const obsCrossfilter = new AnnoMatrixObsCrossfilter(annoMatrix);
|
||||
@@ -242,6 +265,7 @@ export default {
|
||||
annotationRenameLabelInCategory: annoActions.annotationRenameLabelInCategory,
|
||||
annotationLabelCurrentSelection: annoActions.annotationLabelCurrentSelection,
|
||||
saveObsAnnotationsAction: annoActions.saveObsAnnotationsAction,
|
||||
saveGenesetsAction: annoActions.saveGenesetsAction,
|
||||
needToSaveObsAnnotations: annoActions.needToSaveObsAnnotations,
|
||||
layoutChoiceAction: embActions.layoutChoiceAction,
|
||||
setCellSetFromSelection: selnActions.setCellSetFromSelection,
|
||||
|
||||
@@ -5,11 +5,18 @@ import FilenameDialog from "./filenameDialog";
|
||||
|
||||
@connect((state) => ({
|
||||
annotations: state.annotations,
|
||||
saveInProgress: state.autosave?.saveInProgress ?? false,
|
||||
obsAnnotationSaveInProgress:
|
||||
state.autosave?.obsAnnotationSaveInProgress ?? false,
|
||||
genesetSaveInProgress: state.autosave?.genesetSaveInProgress ?? false,
|
||||
error: state.autosave?.error,
|
||||
writableCategoriesEnabled: state.config?.parameters?.annotations ?? false,
|
||||
writableGenesetsEnabled: !(
|
||||
state.config?.parameters?.["annotations_genesets_readonly"] ?? true
|
||||
),
|
||||
annoMatrix: state.annoMatrix,
|
||||
genesets: state.genesets,
|
||||
lastSavedAnnoMatrix: state.autosave?.lastSavedAnnoMatrix,
|
||||
lastSavedGenesets: state.autosave?.lastSavedGenesets,
|
||||
}))
|
||||
class Autosave extends React.Component {
|
||||
constructor(props) {
|
||||
@@ -20,11 +27,11 @@ class Autosave extends React.Component {
|
||||
}
|
||||
|
||||
componentDidMount() {
|
||||
const { writableCategoriesEnabled } = this.props;
|
||||
const { writableCategoriesEnabled, writableGenesetsEnabled } = this.props;
|
||||
|
||||
let { timer } = this.state;
|
||||
if (timer) clearInterval(timer);
|
||||
if (writableCategoriesEnabled) {
|
||||
if (writableCategoriesEnabled || writableGenesetsEnabled) {
|
||||
timer = setInterval(this.tick, 2500);
|
||||
} else {
|
||||
timer = null;
|
||||
@@ -38,18 +45,40 @@ class Autosave extends React.Component {
|
||||
}
|
||||
|
||||
tick = () => {
|
||||
const { dispatch, saveInProgress } = this.props;
|
||||
if (this.needToSave() && !saveInProgress) {
|
||||
const {
|
||||
dispatch,
|
||||
obsAnnotationSaveInProgress,
|
||||
genesetSaveInProgress,
|
||||
} = this.props;
|
||||
if (!obsAnnotationSaveInProgress && this.needToSaveObsAnnotations()) {
|
||||
dispatch(actions.saveObsAnnotationsAction());
|
||||
}
|
||||
if (!genesetSaveInProgress && this.needToSaveGenesets()) {
|
||||
dispatch(actions.saveGenesetsAction());
|
||||
}
|
||||
};
|
||||
|
||||
needToSave = () => {
|
||||
/* return true if we need to save, false if we don't */
|
||||
needToSaveObsAnnotations = () => {
|
||||
/* return true if we need to save obs cell labels, false if we don't */
|
||||
const { annoMatrix, lastSavedAnnoMatrix } = this.props;
|
||||
return actions.needToSaveObsAnnotations(annoMatrix, lastSavedAnnoMatrix);
|
||||
};
|
||||
|
||||
needToSaveGenesets = () => {
|
||||
/* return true if we need to save gene ses, false if we do not */
|
||||
const { genesets, lastSavedGenesets } = this.props;
|
||||
return genesets.initialized && genesets !== lastSavedGenesets;
|
||||
};
|
||||
|
||||
needToSave() {
|
||||
return this.needToSaveGenesets() || this.needToSaveObsAnnotations();
|
||||
}
|
||||
|
||||
saveInProgress() {
|
||||
const { obsAnnotationSaveInProgress, genesetSaveInProgress } = this.props;
|
||||
return obsAnnotationSaveInProgress || genesetSaveInProgress;
|
||||
}
|
||||
|
||||
statusMessage() {
|
||||
const { error } = this.props;
|
||||
if (error) {
|
||||
@@ -61,12 +90,12 @@ class Autosave extends React.Component {
|
||||
render() {
|
||||
const {
|
||||
writableCategoriesEnabled,
|
||||
saveInProgress,
|
||||
writableGenesetsEnabled,
|
||||
lastSavedAnnoMatrix,
|
||||
} = this.props;
|
||||
const initialDataLoadComplete = lastSavedAnnoMatrix;
|
||||
|
||||
if (!writableCategoriesEnabled) return null;
|
||||
if (!writableCategoriesEnabled && !writableGenesetsEnabled) return null;
|
||||
|
||||
return (
|
||||
<div
|
||||
@@ -74,7 +103,7 @@ class Autosave extends React.Component {
|
||||
data-testclass={
|
||||
!initialDataLoadComplete
|
||||
? "autosave-init"
|
||||
: this.needToSave() || saveInProgress
|
||||
: this.saveInProgress() || this.needToSave()
|
||||
? "autosave-incomplete"
|
||||
: "autosave-complete"
|
||||
}
|
||||
|
||||
@@ -1,17 +1,25 @@
|
||||
const Autosave = (
|
||||
state = {
|
||||
saveInProgress: false,
|
||||
error: false,
|
||||
// cell labels
|
||||
obsAnnotationSaveInProgress: false,
|
||||
lastSavedAnnoMatrix: null,
|
||||
|
||||
// gene sets
|
||||
genesetSaveInProgress: false,
|
||||
lastSavedGenesets: null,
|
||||
|
||||
// error state
|
||||
error: false,
|
||||
},
|
||||
action
|
||||
action,
|
||||
nextSharedState
|
||||
) => {
|
||||
switch (action.type) {
|
||||
case "annoMatrix: init complete": {
|
||||
return {
|
||||
...state,
|
||||
error: false,
|
||||
saveInProgress: false,
|
||||
obsAnnotationSaveInProgress: false,
|
||||
lastSavedAnnoMatrix: action.annoMatrix,
|
||||
};
|
||||
}
|
||||
@@ -19,7 +27,7 @@ const Autosave = (
|
||||
case "writable obs annotations - save started": {
|
||||
return {
|
||||
...state,
|
||||
saveInProgress: true,
|
||||
obsAnnotationSaveInProgress: true,
|
||||
};
|
||||
}
|
||||
|
||||
@@ -27,7 +35,7 @@ const Autosave = (
|
||||
return {
|
||||
...state,
|
||||
error: action.message,
|
||||
saveInProgress: false,
|
||||
obsAnnotationSaveInProgress: false,
|
||||
};
|
||||
}
|
||||
|
||||
@@ -35,12 +43,45 @@ const Autosave = (
|
||||
const { lastSavedAnnoMatrix } = action;
|
||||
return {
|
||||
...state,
|
||||
saveInProgress: false,
|
||||
obsAnnotationSaveInProgress: false,
|
||||
error: false,
|
||||
lastSavedAnnoMatrix,
|
||||
};
|
||||
}
|
||||
|
||||
case "geneset: initial load": {
|
||||
return {
|
||||
...state,
|
||||
genesetSaveInProgress: false,
|
||||
lastSavedGenesets: nextSharedState.genesets,
|
||||
};
|
||||
}
|
||||
|
||||
case "autosave: genesets started": {
|
||||
return {
|
||||
...state,
|
||||
genesetSaveInProgress: true,
|
||||
};
|
||||
}
|
||||
|
||||
case "autosave: genesets error": {
|
||||
return {
|
||||
...state,
|
||||
genesetSaveInProgress: false,
|
||||
error: action.message,
|
||||
};
|
||||
}
|
||||
|
||||
case "autosave: genesets complete": {
|
||||
const { lastSavedGenesets } = action;
|
||||
return {
|
||||
...state,
|
||||
genesetSaveInProgess: false,
|
||||
error: false,
|
||||
lastSavedGenesets,
|
||||
};
|
||||
}
|
||||
|
||||
default:
|
||||
return { ...state };
|
||||
}
|
||||
|
||||
@@ -0,0 +1,349 @@
|
||||
/**
|
||||
* Gene set state. Geneset UI state is in a different reducer.
|
||||
*
|
||||
* geneset reducer state is a Map object, where:
|
||||
* key: the geneset name, a string.
|
||||
* val: the geneset defined as an object ("geneset object")
|
||||
*
|
||||
* A geneset object is:
|
||||
* {
|
||||
* genesetName: <string> # same as the map key
|
||||
* genesetDescription: <string>
|
||||
* genes: Map<<string>, {
|
||||
* geneSymbol: <string>, # same as the map key
|
||||
* geneDescription: <string>
|
||||
* }>
|
||||
* }
|
||||
*
|
||||
* Geneset and genes Map order is significant, and will be preserved across
|
||||
* CRUD operations on either.
|
||||
*
|
||||
* This reducer does light error checking, but not as much as the backend
|
||||
* routes. Do not rely on it to enforce geneset integrity - eg, no duplicate
|
||||
* genes in a geneset.
|
||||
*/
|
||||
const GeneSets = (
|
||||
state = {
|
||||
initialized: false,
|
||||
lastTid: undefined,
|
||||
genesets: new Map(),
|
||||
},
|
||||
action
|
||||
) => {
|
||||
switch (action.type) {
|
||||
/**
|
||||
* Initial, load-time bootstrap.
|
||||
* {
|
||||
* type: "geneset: initial load"
|
||||
* data: JSON response
|
||||
* }
|
||||
*/
|
||||
case "geneset: initial load": {
|
||||
const { data } = action;
|
||||
|
||||
if (
|
||||
!data ||
|
||||
typeof data.tid !== "number" ||
|
||||
!Array.isArray(data.genesets)
|
||||
)
|
||||
throw new Error("missing or malformed JSON response");
|
||||
|
||||
const lastTid = data.tid;
|
||||
const genesetsData = data.genesets;
|
||||
const genesets = new Map();
|
||||
|
||||
for (const gsData of genesetsData) {
|
||||
const genes = new Map();
|
||||
for (const gene of gsData.genes) {
|
||||
genes.set(gene.gene_symbol, {
|
||||
geneSymbol: gene.gene_symbol,
|
||||
geneDescription: gene?.["gene_description"] ?? "",
|
||||
});
|
||||
}
|
||||
const gs = {
|
||||
genesetName: gsData.geneset_name,
|
||||
genesetDescription: gsData?.["geneset_description"] ?? "",
|
||||
genes,
|
||||
};
|
||||
genesets.set(gsData.geneset_name, gs);
|
||||
}
|
||||
|
||||
return {
|
||||
initialized: true,
|
||||
lastTid,
|
||||
genesets,
|
||||
};
|
||||
}
|
||||
|
||||
/**
|
||||
* Creates a new & empty geneset with the given name and description.
|
||||
* {
|
||||
* type: "geneset: create",
|
||||
* genesetName: string, // gene set name
|
||||
* genesetDescription: string, // geneset description
|
||||
* }
|
||||
*
|
||||
*/
|
||||
case "geneset: create": {
|
||||
const { genesetName, genesetDescription } = action;
|
||||
if (
|
||||
typeof genesetName !== "string" ||
|
||||
!genesetName ||
|
||||
genesetDescription === undefined
|
||||
)
|
||||
throw new Error("geneset: create -- name or description unspecified.");
|
||||
if (state.genesets.has(genesetName))
|
||||
throw new Error("geneset: create -- name already defined.");
|
||||
|
||||
const genesets = new Map(state.genesets); // clone
|
||||
genesets.set(genesetName, {
|
||||
genesetName,
|
||||
genesetDescription,
|
||||
genes: new Map(),
|
||||
});
|
||||
|
||||
return {
|
||||
...state,
|
||||
genesets,
|
||||
};
|
||||
}
|
||||
|
||||
/**
|
||||
* Deletes the named geneset, if it exists. Throws if it does not.
|
||||
* {
|
||||
* type: "geneset: delete",
|
||||
* genesetName: string
|
||||
* }
|
||||
*/
|
||||
case "geneset: delete": {
|
||||
const { genesetName } = action;
|
||||
if (!state.genesets.has(genesetName))
|
||||
throw new Error("geneset: delete -- geneset name does not exist.");
|
||||
|
||||
const genesets = new Map(state.genesets); // clone
|
||||
genesets.delete(genesetName);
|
||||
return {
|
||||
...state,
|
||||
genesets,
|
||||
};
|
||||
}
|
||||
|
||||
/**
|
||||
* Update the named geneset with a new name and description. Preserves the existing
|
||||
* order of the geneset, even when the genesetName changes.
|
||||
* {
|
||||
* type: "geneset: update",
|
||||
* genesetName: string, current name of geneset to be updated
|
||||
* update: {
|
||||
* genesetName: string, new name
|
||||
* genesetDescription: string, new description
|
||||
* }
|
||||
* }
|
||||
*
|
||||
* For example, if you want to update JUST the description:
|
||||
* dispatch({
|
||||
* action: "geneset: update",
|
||||
* genesetName: "foo",
|
||||
* update: { genesetName: "foo", genesetDescription: "a new description"}
|
||||
* })
|
||||
*/
|
||||
case "geneset: update": {
|
||||
const { genesetName, update } = action;
|
||||
if (
|
||||
typeof genesetName !== "string" ||
|
||||
!genesetName ||
|
||||
!state.genesets.has(genesetName)
|
||||
)
|
||||
throw new Error(
|
||||
"geneset: update -- geneset name unspecified or does not exist."
|
||||
);
|
||||
if (state.genesets.has(update.genesetName))
|
||||
throw new Error("geneset: update -- update specified existing name.");
|
||||
|
||||
const prevGs = state.genesets.get(genesetName);
|
||||
const newGs = {
|
||||
...update,
|
||||
genes: prevGs.genes,
|
||||
}; // clone
|
||||
|
||||
// clone the map, preserving current insert order, but mapping name->newName.
|
||||
const genesets = new Map();
|
||||
for (const [name, gs] of state.genesets) {
|
||||
if (name === genesetName) genesets.set(newGs.genesetName, newGs);
|
||||
else genesets.set(name, gs);
|
||||
}
|
||||
|
||||
return {
|
||||
...state,
|
||||
genesets,
|
||||
};
|
||||
}
|
||||
|
||||
/**
|
||||
* Adds genes to the geneset. They are appended to the END of the geneset, in the
|
||||
* order provided. Duplicates or genes already in the geneset, will be ignored.
|
||||
* {
|
||||
* type: "geneset: add genes"
|
||||
* genesetName: <string>, // gene set name
|
||||
* genes: Array<{
|
||||
* geneSymbol: <string>,
|
||||
* geneDescription: <string>
|
||||
* }>
|
||||
* }
|
||||
*
|
||||
* Example:
|
||||
* dispatch({
|
||||
* type: "add genes",
|
||||
* genesetName: "foo",
|
||||
* genes: [ { geneSymbol: "FOXP", geneDescription: "test" }]
|
||||
* });
|
||||
*/
|
||||
case "geneset: add genes": {
|
||||
const { genesetName, genes } = action;
|
||||
if (!state.genesets.has(genesetName))
|
||||
throw new Error("geneset: add genes -- geneset name does not exist.");
|
||||
|
||||
// clone
|
||||
const genesets = new Map(state.genesets);
|
||||
const gs = {
|
||||
...genesets.get(genesetName),
|
||||
genes: new Map(genesets.get(genesetName).genes),
|
||||
};
|
||||
genesets.set(genesetName, gs);
|
||||
|
||||
// add
|
||||
const newGenes = gs.genes;
|
||||
for (const gene of genes) {
|
||||
const { geneSymbol } = gene;
|
||||
const geneDescription = gene?.geneDescription ?? "";
|
||||
// ignore genes already present
|
||||
if (!newGenes.has(geneSymbol))
|
||||
newGenes.set(geneSymbol, {
|
||||
geneSymbol,
|
||||
geneDescription,
|
||||
});
|
||||
}
|
||||
|
||||
return {
|
||||
...state,
|
||||
genesets,
|
||||
};
|
||||
}
|
||||
|
||||
/**
|
||||
* Delete genes from the named geneset. Will throw if the genesetName does
|
||||
* not exist. Will ignore geneSymbols that do not exist.
|
||||
* {
|
||||
* type: "geneset: delete genes",
|
||||
* genesetName: <string>, // the geneset from which to delete genes
|
||||
* geneSymbols: [<string>, ...], // the gene symbols to delete.
|
||||
* }
|
||||
*
|
||||
* Example:
|
||||
* dispatch({
|
||||
* type: "geneset: delete genes",
|
||||
* genesetName: "a geneset name",
|
||||
* geneSymbols: ["F5"]
|
||||
* })
|
||||
*/
|
||||
case "geneset: delete genes": {
|
||||
const { genesetName, geneSymbols } = action;
|
||||
if (!state.genesets.has(genesetName))
|
||||
throw new Error(
|
||||
"geneset: delete genes -- geneset name does not exist."
|
||||
);
|
||||
|
||||
// clone
|
||||
const genesets = new Map(state.genesets);
|
||||
const gs = {
|
||||
...genesets.get(genesetName),
|
||||
genes: new Map(genesets.get(genesetName).genes),
|
||||
};
|
||||
genesets.set(genesetName, gs);
|
||||
|
||||
// delete
|
||||
const { genes } = gs;
|
||||
for (const geneSymbol of geneSymbols) {
|
||||
genes.delete(geneSymbol);
|
||||
}
|
||||
return {
|
||||
...state,
|
||||
genesets,
|
||||
};
|
||||
}
|
||||
|
||||
/**
|
||||
* Set/update the description of the gene. NOTE that this does not allow the name
|
||||
* of the gene to change - only "geneset: add" and "geneset: delete" can change
|
||||
* the genes in a geneset. Use this to update a gene description AFTER you add it
|
||||
* to the geneset.
|
||||
* {
|
||||
* type: "geneset: set gene description",
|
||||
* genesetName: <string>, // the geneset to update
|
||||
* update: {
|
||||
* geneSymbol: <string>, // the gene to update, MUST exist already in the geneset
|
||||
* geneDescription: <string>
|
||||
* }
|
||||
* }
|
||||
*
|
||||
* Example:
|
||||
* dispatch({
|
||||
* type: "geneset: set gene description",
|
||||
* genesetName: "my fav geneset",
|
||||
* update: {
|
||||
* geneSymbol: "F5",
|
||||
* geneDescription: "tada, moar description"
|
||||
* }
|
||||
* })
|
||||
*/
|
||||
case "geneset: set gene description": {
|
||||
const { genesetName, update } = action;
|
||||
if (!state.genesets.has(genesetName))
|
||||
throw new Error(
|
||||
"geneset: set gene description -- geneset name does not exist."
|
||||
);
|
||||
|
||||
// clone
|
||||
const genesets = new Map(state.genesets);
|
||||
const gs = {
|
||||
...genesets.get(genesetName),
|
||||
genes: new Map(genesets.get(genesetName).genes),
|
||||
};
|
||||
genesets.set(genesetName, gs);
|
||||
|
||||
const { geneSymbol, geneDescription } = update;
|
||||
const gene = gs.genes.get(geneSymbol);
|
||||
if (!gene)
|
||||
throw new Error("geneset: set gene description -- no such gene");
|
||||
gs.genes.set(geneSymbol, {
|
||||
geneSymbol,
|
||||
geneDescription,
|
||||
});
|
||||
|
||||
return {
|
||||
...state,
|
||||
genesets,
|
||||
};
|
||||
}
|
||||
|
||||
/**
|
||||
* Used by autosave to update the server synchronization TID
|
||||
*/
|
||||
case "geneset: set tid": {
|
||||
const { tid } = action;
|
||||
if (!Number.isInteger(tid) || tid < 0)
|
||||
throw new Error("TID must be a positive integer number");
|
||||
if (state.lastTid !== undefined && tid < state.lastTid)
|
||||
throw new Error("TID may not be decremented.");
|
||||
return {
|
||||
...state,
|
||||
lastTid: tid,
|
||||
};
|
||||
}
|
||||
|
||||
default:
|
||||
return state;
|
||||
}
|
||||
};
|
||||
|
||||
export default GeneSets;
|
||||
@@ -15,6 +15,7 @@ import differential from "./differential";
|
||||
import layoutChoice from "./layoutChoice";
|
||||
import controls from "./controls";
|
||||
import annotations from "./annotations";
|
||||
import genesets from "./genesets";
|
||||
import autosave from "./autosave";
|
||||
import ontology from "./ontology";
|
||||
import centroidLabels from "./centroidLabels";
|
||||
@@ -31,6 +32,7 @@ const Reducer = undoable(
|
||||
["obsCrossfilter", obsCrossfilter],
|
||||
["ontology", ontology],
|
||||
["annotations", annotations],
|
||||
["genesets", genesets],
|
||||
["layoutChoice", layoutChoice],
|
||||
["categoricalSelection", categoricalSelection],
|
||||
["continuousSelection", continuousSelection],
|
||||
@@ -55,6 +57,7 @@ const Reducer = undoable(
|
||||
"differential",
|
||||
"layoutChoice",
|
||||
"centroidLabels",
|
||||
"genesets",
|
||||
"annotations",
|
||||
],
|
||||
undoableConfig
|
||||
|
||||
@@ -108,7 +108,7 @@ class AnnotationsLocalFile(Annotations):
|
||||
def read_genesets(self, data_adaptor, context=None):
|
||||
if has_request_context():
|
||||
if not current_app.auth.is_user_authenticated():
|
||||
return ([], None)
|
||||
return ({}, self.last_geneset_tid)
|
||||
|
||||
fname = self._get_genesets_filename(data_adaptor)
|
||||
genesets = {}
|
||||
@@ -165,7 +165,7 @@ class AnnotationsLocalFile(Annotations):
|
||||
|
||||
output_file = self.label_output_file or self.genesets_output_file
|
||||
if output_file:
|
||||
return os.path.dirname(self.path.abspath(output_file))
|
||||
return os.path.dirname(os.path.abspath(output_file))
|
||||
|
||||
return os.getcwd()
|
||||
|
||||
|
||||
Reference in New Issue
Block a user